1,726,188 research outputs found
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081
No full textThis work was supported by The Wellcome Trust.The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0: 8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens.Peer reviewe
FAA-S-8081-6D Flight Instructor Airplane Practical Test Standards
No full textMaterial in FAA-S-8081-6D will be effective December 1, 2012. All previous editions of Flight Instructor – Airplane Practical Test Standards will be obsolete as of this date. FAA-S-8081-6D (this page intentionally left blank) FAA-S-8081-6D Forward The Flight Instructor—Airplane Practical Test Standards book has been published by the Federal Aviation Administration (FAA) to establish the standards for the flight instructor certification practical tests for the airplane category and the single-engine and multiengine classes. FAA inspectors and designated pilot examiners shall conduct practical tests in compliance with these standards. Flight instructors and applicants should find these standards helpful in practical test preparation
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081
No full textThe human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending
from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the
genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8;
biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis
reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a
plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has
provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the
high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide
new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes
potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in
the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are
absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients
used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate
respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y.
enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into
the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations
looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution
of other human enteropathogens
Linked collectors and determiners for: Afroneutria, a new spider genus of Afrotropical Ctenidae (Arachnida, Araneae).
No full textNatural history specimen data linked to collectors and determiners held within, "Afroneutria, a new spider genus of Afrotropical Ctenidae (Arachnida, Araneae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f">https://bionomia.net/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f">https://gbif.org/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f</a>. Formatted as a Frictionless Data package
Circular Representation of the Y. enterocolitica Strain 8081 Chromosome
No full text<div><p>The outer scale shows the size in bps. From the outside in, circles 1 and 2 show the position of CDSs transcribed in a clockwise and anticlockwise direction, respectively (for colour codes see below). Circles 3–5 (all CDSs coloured green) mark the position of Y. enterocolitica strain 8081 genes that have orthologues (by reciprocal FASTA analysis) in Y. pestis strains CO92, 91001, and KIM10+ and in (circle 6) Y. pseudotuberculosis strain IP32953 (CDSs coloured orange), respectively. Circles 7–10 show the Y. enterocolitica strain 8081 CDSs present (as detected by microarray) in all of the Y. enterocolitica isolates tested from biotype 1A (eight strains, red), biotype 2 (two strains, pink), biotype 3 (eight strains, blue), and biotype 4 (eight strains, yellow). Circle 11 shows CDSs unique to Y. enterocolitica strain 8081 (brown) compared with Y. pestis strain CO92 and Y. pseudotuberculosis strain IP32953 as determined by reciprocal FASTA analysis. Circle 12 shows CDSs unique to Y. enterocolitica strain 8081 (black) biotype 1B compared to all isolates of Y. enterocolitica biotypes 1A, 2, 3, and 4 as determined by microarray analysis. Circle 13 shows a plot of G + C content (in a 10-kb window) and circle 14 shows a plot of GC skew ([G − C]/[G + C] in a 10-kb window). Genes in circles 1 and 2 are colour-coded according to the function of their gene products: dark green, membrane or surface structures; yellow, central or intermediary metabolism; cyan, degradation of macromolecules; red, information transfer/cell division; cerise, degradation of small molecules; pale blue, regulators; salmon pink, pathogenicity or adaptation; black, energy metabolism; orange, conserved hypothetical; pale green, unknown; and brown, pseudogenes. The position of prophage elements (pink) and other important regions of difference (mentioned in the text) are marked (red). See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020206#pgen-0020206-t002" target="_blank">Table 2</a> for a description.</p><p>LPS, lipopolysaccharide biosynthetic genes.</p></div
Linked collectors and determiners for: Afroneutria, a new spider genus of Afrotropical Ctenidae (Arachnida, Araneae).
No full textNatural history specimen data linked to collectors and determiners held within, "Afroneutria, a new spider genus of Afrotropical Ctenidae (Arachnida, Araneae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f">https://bionomia.net/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f">https://gbif.org/dataset/7d852af3-8081-473d-98d3-4ab4e09d3c0f</a>. Formatted as a Frictionless Data package
Linked collectors and determiners for: Freshwater Gastropods of Taveuni.
No full textNatural history specimen data linked to collectors and determiners held within, "Freshwater Gastropods of Taveuni". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/ffa7390a-800c-4b37-8081-e5352e0310c7">https://bionomia.net/dataset/ffa7390a-800c-4b37-8081-e5352e0310c7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ffa7390a-800c-4b37-8081-e5352e0310c7">https://gbif.org/dataset/ffa7390a-800c-4b37-8081-e5352e0310c7</a>. Formatted as a Frictionless Data package
Novel insights into the quorum sensing system of Yersina enterocolitica 8081
No full textY. enterocolitica possesses an N-acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) system which consists of the luxRI homologues, yenRI. The objective of this project was to increase our understanding of the QS system(s) in Y. enterocolitica by characterising the AHL-dependent system on a genus wide basis. Species-wide analysis of an Y. enterocolitica multi-strain genome database revealed an additional luxR homologue, we termed yeoR, which is present in the fully sequenced, highly virulent Y. enterocolitica 8081 strain and other USA strains but absent in UK strains. This indicates genetic differences in the QS systems of 'New World' (North America)and 'Old World' (Europe and Japan) strains of Y. enterocolitica. yeoR is an 'orphan' luxR homologue which is not associated with an adjacent luxI homologue. Consequent work described in this study focused on the Y. enterocolitica 8081 strain. LC-mass spectrometry of spent culture supernatants from Y. enterocolitica 8081 grown at 30°C identified 16 different AHLs, mainly N-(3-oxohexanoyl)-L-homoserine lactone (62.4%) and N-hexanoyl-L-homoserine lactone (27.4%). 11 of the 16 AHLs had not previously been documented for this bacterium, including N-(3-oxoheptanoyl)-Lhomo serine lactone (with an odd number of carbons in the acyl chain) which constituted 5.1 % and has rarely been documented previously.
The lambda red recombinase method of mutagenesis was used for the rapid generation of QS mutants in Y. enterocolitica 8081. Seven QS mutants were generated, three were single mutants: deltayenI deltayenR and deltayeoR, three were double mutants: deltayenIyenR, deltayenIyeoR and deltayenRyeoR, and one was a triple mutant: deltayenIyenRycoR. Analysis of the QS mutants revealed that the level of AHLs synthesised at 30°C by the R mutants: deltayenR, deltayeoR and deltayenRyeoR, were similar to the wildtype while for AHL synthase mutants: deltayenI, deltayenIyenR, deltayenIycoR and deltayenIyenRyeoR, levels of AHL were greatly reduced compared with the wildtype but were not entirely abolished.
Transcriptomic analysis of Y.enterocolitica 8081 wildtype and its QS mutants using microarray technology revealed many possible QS-related regulatory networks including motility, type III secretion system and High Pathogenicity Island. Microarray data, together with RQ-PCR, phenotypic studies and promoter fusion studies showed that QS is correlated with virulence regulation (expression of virF and tyeA), virulence factors (expression of yadA and invA) and maintenance of the pYVe plasmid (expression of repA and spyA), which have not been previously documented.
In conclusion, this study revealed that Y. enterocolitica 8081 has a sophisticated QS system which consists of the AHL synthase, YenI and two LuxR-type regulators, YenR and Y coR working in tandem and sharing overlapping regulon. This system maybe linked to the hypervirulence in the 8081 strain but further work is needed to confirm this
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
- …
